Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Runx1

Cell type

Cell type Class
Blood
Cell type
B cells
NA
NA

Attributes by original data submitter

Sample

source_name
resting B cells isolated from spleen
strain
C57BL/6
genotype
WT
cell type
Resting B cells
chip antibody
RUNX1 (Abcam- ab23980)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Spleens were isolated from 6- to 10-week-old C57B6 mice and homogenized through a sieve in B cell culture medium (RPMI-1640 (Lonza), 10% fetal calf serum (FCS) (Sigma), 0.1 U/ml penicillin (Lonza), 0.1 μg/ml streptomycin (Lonza), 2mM L-Glutamine (Lonza), 50μM beta-mercaptoethanol (Gibco)). The cell suspension was centrifuged on a Ficoll-Paque (GE Healthcare) cushion and the buffy coat layer was resuspended at a concentration of 1x 10e8 cells/ml in PBS + 2% FCS/ 1mM EDTA. Resting B cells were isolated using an EasySep Negative Selection- Mouse B Cell Isolation Kit (STEMCELL Technologies), which depletes for non-B cell markers and activated CD43+ B cells. 5ng of ChIP/Input DNA was used to prepare libraries using the NEBNext® Ultra™ II DNA LibraryPrep Kit for Illumina following the manufacturer recommendations. Library quality and quantity were assessed on a Bioanalyser and Qubit, respectively. Libraries were sequenced on an Illumina Hiseq 2500 (v4 chemistry), and single-end 50bp reads or paired-end 100bp reads per sample were generated.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
39533898
Reads aligned (%)
97.7
Duplicates removed (%)
14.4
Number of peaks
8865 (qval < 1E-05)

mm9

Number of total reads
39533898
Reads aligned (%)
97.5
Duplicates removed (%)
14.4
Number of peaks
9294 (qval < 1E-05)

Base call quality data from DBCLS SRA